Comparative Genomics of an Emerging Amphibian Virus

Brendan Epstein; Andrew Storfer

doi:10.1534/g3.115.023762

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Comparative Genomics of an Emerging Amphibian Virus

Journal article

Open access

Comparative Genomics of an Emerging Amphibian Virus

Brendan Epstein and Andrew Storfer

G3 (Bethesda, Md.), Vol.6(1), pp.15-27

11/03/2015

DOI: https://doi.org/10.1534/g3.115.023762

Handle:

https://hdl.handle.net/2376/105036

PMCID: PMC4704714

PMID: 26530419

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https://doi.org/10.1534/g3.115.023762View

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Abstract

Geography

Genetics, Population

Genome, Viral

Computational Biology - methods

Ranavirus - genetics

Molecular Sequence Annotation

Selection, Genetic

Phylogeny

Ranavirus - classification

Genetic Variation

Amphibians - virology

Animals

Recombination, Genetic

Genome Size

Ambystoma

Bayes Theorem

High-Throughput Nucleotide Sequencing

Genomics - methods

Genetic Structures

Ranavirus - isolation & purification

Ranaviruses, a genus of the Iridoviridae, are large double-stranded DNA viruses that infect cold-blooded vertebrates worldwide. Ranaviruses have caused severe epizootics in commercial frog and fish populations, and are currently classified as notifiable pathogens in international trade. Previous work shows that a ranavirus that infects tiger salamanders throughout Western North America (Ambystoma tigrinum virus, or ATV) is in high prevalence among salamanders in the fishing bait trade. Bait ATV strains have elevated virulence and are transported long distances by humans, providing widespread opportunities for pathogen pollution. We sequenced the genomes of 15 strains of ATV collected from tiger salamanders across western North America and performed phylogenetic and population genomic analyses and tests for recombination. We find that ATV forms a monophyletic clade within the rest of the Ranaviruses and that it likely emerged within the last several thousand years, before human activities influenced its spread. We also identify several genes under strong positive selection, some of which appear to be involved in viral virulence and/or host immune evasion. In addition, we provide support for the pathogen pollution hypothesis with evidence of recombination among ATV strains, and potential bait-endemic strain recombination.

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Title: Comparative Genomics of an Emerging Amphibian Virus
Creators: Brendan Epstein - School of Biological Sciences, Washington State University, Pullman, Washington 99164
Andrew Storfer - School of Biological Sciences, Washington State University, Pullman, Washington 99164 astorfer@wsu.edu
Publication Details: G3 (Bethesda, Md.), Vol.6(1), pp.15-27
Academic Unit: Biological Sciences, School of
Publisher: United States
Identifiers: 99900546635701842
Language: English
Resource Type: Journal article